Undiagnosed Diseases Program Research Articles

PARK7-Related Early Onset Parkinson Disease in the Setting of Complete Uniparental Isodisomy of Chromosome 1.

Approximately 10% of Parkinson disease (PD) has a monogenic basis. PARK7 is a rare recessive form of early-onset PD caused by mutations in the gene PARK7 (formerly DJ1 ).1 As expected for a recessive disorder, PARK7 patients usually inherit 1 mutant allele from each parent; in fact, most reported cases have occurred in consanguineous families. We report an adult with early onset PD who inherited 2 identical pathogenic PARK7 variants from her asymptomatic father, a carrier for the same variant, via complete uniparental isodisomy (UPD) of chromosome 1. The authors wish to thank patients, families, consultants, and referring physicians participating in the NIH Undiagnosed Diseases Program.

Postzygotic inactivating mutation of KIF13Alocated at chromosome 6p22.3 in a patient with a novel mosaic neuroectodermal syndrome.

Hypomelanosis of Ito (HMI) is part of a neuroectodermal syndrome characterized by distinctive skin manifestations with or without multisystemic involvements. In our undiagnosed diseases program, we have encountered a 3-year-old girl presenting with characteristic skin hypopigmentation suggesting HMIand developmental delay. An exome and genome approach utilizing next-generation sequencing revealed a heterozygous de novo frameshift variant in the KIF13A gene, i.e., NM_022113.6: c.2357dupA, resulting in nonsense-mediated decay. The low mutant allelic ratio suggested that the mutation has occurred postzygotically leading to embryonic mosaicism. Functionally, K1F3A regulates cell membrane blebbing and migration of neural crest cells by controlling recycling of RHOB to the plasma membrane and is also involved in melanosome biogenesis. Importantly, hypopigmentation of the skin has been reported in chr 6p22.3-p23 microdeletion syndrome supporting the association of KIF13A haploinsufficiency with the novel neuroectodermal syndrome. With the increased availability of genome sequencing, we envisage more genetic causes of HMI will be identified in the future.

Spectrum of movement disorders in GNAO1 encephalopathy: in-depth phenotyping and case-by-case analysis

BackgroundGNAO1 encephalopathy is a rare neurodevelopmental disorder characterized by distinct movement presentations and early onset epileptic encephalopathy. Here, we report the in-depth phenotyping of genetically confirmed patients with GNAO1 encephalopathy, focusing on movement presentations.ResultsSix patients who participated in Korean Undiagnosed Disease Program were diagnosed to have pathogenic or likely pathogenic variants in GNAO1 using whole exome sequencing. All medical records and personal video clips were analyzed with a literature review. Three of the 6 patients were male. Median follow-up duration was 41 months (range 7–78 months) and age at last examination was 7.4 years (range 3.3–16.9 years). Initial complaints were hypotonia or developmental delay in 5 and right-hand clumsiness in 1 patient, which were noticed at median age of 3 months (range 0–75 months). All patients showed global developmental delay and 4 had severely retarded development. Five patients (5/6, 83.3%) had many different movement symptoms with various onset and progression. The symptoms included stereotyped hands movement, non-epileptic myoclonus, dyskinesia, dystonia and choreoathetosis. Whole exome sequencing identified 6 different variants in GNAO1. Three were novel de novo variants and atypical presentation was noted in a patient. One variant turned out to be inherited from patient’s mother who had mosaic variant. Distinct and characteristics movement phenotypes in patients with variant p.Glu246Lys and p.Arg209His were elucidated by in-depth phenotyping and literature review.ConclusionsWe reported 6 patients with GNAO1 encephalopathy showing an extremely diverse clinical spectrum on video. Some characteristic movement features identified by careful inspection may also provide important diagnostic insight and practice guidelines.

SMART Work Design: Accelerating the Diagnosis of Rare Diseases in the Western Australian Undiagnosed Diseases Program.

The accurate and efficient diagnosis of rare diseases, many of which include congenital anomalies, depends largely on the specialists who diagnose them – including their ability to work alongside specialists from other fields and to take full advantage of cutting-edge precision medicine technologies and precision public health approaches. However, highly specialized clinicians operating within a historically-siloed healthcare system is antithetical to the multi-disciplinary, collaborative, and creative approach that facilitates the diagnosis of rare diseases. The Western Australian Undiagnosed Diseases Program (UDP-WA) successfully re-designed the work of the involved clinicians to facilitate teamworking across silos. To understand the effectiveness of the Western Australian program, we draw on a SMART work design perspective (i.e., work that involves Stimulation, Mastery, Agency, Relations, and Tolerable demands). We propose that the redesign was successful in part because it improved crucial psychosocial work characteristics that are less prevalent in the broader work system, as identified in the SMART model. Based on the effectiveness of UDP-WA and its SMART design, we provide a framework that clinicians, healthcare managers, and policymakers can consider when they re-design work so that they can create SMART jobs within healthcare.

Singapore Undiagnosed Disease Program: Genomic Analysis aids Diagnosis and Clinical Management

ObjectiveUse next-generation sequencing (NGS) technology to improve our diagnostic yield in patients with suspected genetic disorders in the Asian setting.DesignA diagnostic study conducted between 2014 and 2019 (and ongoing) under...

Interrogating Whole Genome Sequences for Repeat Expansion Diseases in the NIH Undiagnosed Diseases Program (4817)

Interrogating Whole Genome Sequences for Repeat Expansion Diseases in the NIH Undiagnosed Diseases Program (4817)

The undiagnosed diseases program: Approach to diagnosis.

Undiagnosed and rare conditions are collectively common and affect millions of people worldwide. The NIH Undiagnosed Diseases Program (UDP) strives to achieve both a comprehensive diagnosis and a better understanding of the mechanisms of disease for many of these individuals. Through the careful review of records, a well-orchestrated inpatient evaluation, genomic sequencing and testing, and with the use of emerging strategies such as matchmaking programs, the UDP succeeds nearly 30 percent of the time for these highly selective cases. Although the UDP process is built on a unique set of resources, case examples demonstrate steps genetic professionals can take, in both clinical and research settings, to arrive at a diagnosis for their most challenging cases.

Diagnosing rare diseases: A sociotechnical approach to the design of complex work systems

How do complex healthcare systems that are organised into distinct speciality areas achieve effective patient care transitions when patients present with a rare constellation of symptoms that affect multiple body systems? How do these patients challenge existing ways of organising tasks, clinical activities, and interdependent responsibilities? The current study applies a sociotechnical systems perspective to understand how these complex work design and care-related challenges were resolved by the Western Australian Undiagnosed Diseases Program. We conducted a two-year longitudinal, qualitative study of this program, conceived to improve the diagnosis and management of patients with rare, multi-system disorders by piloting a re-design of the local system of diagnostic work. Specifically, we (1) compared the configuration and effectiveness of the old system and the re-designed system; and (2) analysed the process of system re-design (i.e., the design, implementation, and operation of the program) in order to understand the factors that contributed to – or inhibited – its success. We discuss the theoretical and practical implications of our findings for effectively re-designing complex, trans-organisational work systems.

Case report: extreme coronary calcifications and hypomagnesemia in a patient with a 17q12 deletion involving HNF1B

Background17q12 deletion syndrome encompasses a broad constellation of clinical phenotypes, including renal magnesium wasting, maturity-onset diabetes of the young (MODY), renal cysts, genitourinary malformations, and neuropsychiatric illness. Manifestations outside of the renal, endocrine, and nervous systems have not been well described.Case presentationWe report a 62-year-old male referred to the Undiagnosed Diseases Program (UDP) at the National Institutes of Health (NIH) who presented with persistent hypermagnesiuric hypomagnesemia and was found to have a 17q12 deletion. The patient exhibited several known manifestations of the syndrome, including severe hypomagnesemia, renal cysts, diabetes and cognitive deficits. Coronary CT revealed extensive coronary calcifications, with a coronary artery calcification score of 12,427. Vascular calcifications have not been previously reported in this condition. We describe several physiologic mechanisms and a review of literature to support the expansion of the 17q12 deletion syndrome to include vascular calcification.ConclusionExtensive coronary and vascular calcifications may be an extension of the 17q12 deletion phenotype, particularly if hypomagnesemia and hyperparathyroidism are prevalent. In patients with 17q12 deletions involving HNF1B, hyperparathyroidism and hypomagnesemia may contribute to significant cardiovascular risk.

A comprehensive, multidisciplinary, precision medicine approach to discover effective therapy for an undiagnosed, progressive, fibroinflammatory disease

Precision medicine has generated diagnoses for many patients with challenging undiagnosed disorders. Some individuals remain without a diagnosis despite comprehensive testing, and this impedes their treatment. This report addresses the role of personalized medicine in identifying effective therapy for an undiagnosed disease. A 22-year-old woman presented with chronic severe recurrent trismus, facial pain, progressive multicentric inflammatory and fibrotic masses, and high C-reactive protein. Sites of disease included the pterygomaxillary region, masseter muscles, mandible, lung, pericardium, intrabdominal cavity, and retroperitoneum. A diagnosis was not established after an extensive assessment, including multiple biopsies. The patient was subsequently evaluated under the Undiagnosed Diseases Program at the National Institutes of Health. Large scale genotyping, proteomic studies, and in vitro and gene expression analyses of fibroblasts obtained from a major disease locus were performed. Germline genetic testing did not identify strong candidate genes; proteomic studies of the patient's serum and bronchoalveolar lavage fluid and gene expression analyses of her cells were consistent with dysregulation of the tumor necrosis factor-alpha pathway. The patient's cultured fibroblasts were incubated with selected drugs, and cell proliferation was inhibited by hydroxychloroquine. Treatment of the patient with hydroxychloroquine conferred prolonged beneficial clinical effects, including stabilization of trismus and reduction of corticosteroid dose, C-reactive protein, and size of masses. This case represents an example of precision medicine applied to discover effective treatments for individuals with enigmatic undiagnosed disorders.

The prevalence and impact of psychiatric symptoms in an undiagnosed diseases clinical program

In 2008, the NIH launched an undiagnosed diseases program to investigate difficult to diagnose, and typically, multi-system diseases. The objective of this study was to evaluate the presence of psychiatric symptoms or psychiatric diagnoses in a cohort of patients seeking care at the Emory Special Diagnostic Service clinic. We hypothesized that psychiatric symptoms would be prevalent and associated with trauma exposure, and a decreased quality of life and functioning. This is a cross-sectional, retrospective analysis of 247 patients seen between February 7, 2014 and May 31, 2017. The sources for data included the Emory Health History Questionnaire (HHQ) that had the work and social adjustment and quality of life enjoyment and satisfaction questionnaire–short form (QLSQ) embedded in it; medical records, and the comprehensive standardized special diagnostic clinic forms. Primary outcomes were presence of any psychiatric symptom, based on report of the symptom on the HHQ or medical record, or presence of a confirmed preexisting psychiatric disorder. Seventy-two percent of patients had at least one psychiatric symptom while 24.3% of patients had a pre-existing psychiatric diagnosis. Patients with any psychiatric symptom had significantly diminished Q-LES-Q scores (45.27 ± 18.63) versus patients with no psychiatric symptoms (62.01 ± 21.57, t = 5.60, df = 225, p<0.0001) and they had significantly greater functional disability. Patients with a psychiatric disorder also had significantly diminished Q-LES-Q scores (45.16 ± 17.28) versus those without a psychiatric diagnosis (51.85 ± 21.54, t = 2.11, df = 225, p = 0.036) but did not have significantly increased functional impairment. Both patients with psychiatric symptoms and ones with psychiatric disorders had an increased prevalence of trauma. Psychiatric symptoms are prevalent in patients evaluated for undiagnosed disorders. The presence of any psychiatric symptom, with or without a formal psychiatric diagnosis, significantly decreases quality of life and functioning. This suggests that assessment for psychiatric symptoms should be part of the evaluation of individuals with undiagnosed disorders and may have important diagnostic and treatment implications.

Medical genetics and genomic medicine in Japan.

Since 1961, all Japanese citizens have belonged to one of the available medical care insurance systems. This "universal care" system has contributed to the maintenance of health: the life expectancy at birth was 84 years in 2016, and the infant mortality rate (the number of infants dying before reaching 1 year of age) was 2.0 per 1,000 live births, which is one of the lowest rates in the world. The Japanese government initiated the National Program on Rare and Intractable Diseases in 1972. This program has promoted research and expanded support for patients with rare and intractable diseases. Registered patients are eligible for a subsidy scheme that helps to cover medical care costs. Among the 331 diseases that are currently included in this program, more than half of the diseases are Mendelian disorders. The National Program on Rare and Intractable Diseases has fostered research in medical genetics in Japan and many causative genes for Mendelian diseases have been identified by Japanese geneticists. Recently, the Japanese government has determined to support several genomic medicine initiatives including the undiagnosed disease program (Initiative on Rare and Undiagnosed Diseases) and pathogenic variant databases.

The Korean undiagnosed diseases program: lessons from a one-year pilot project

BackgroundThe Korean Undiagnosed Diseases Program (KUDP) was launched in January 2017 as a one-year pilot project to address the increasing global interest in patients with undiagnosed rare diseases. The purpose of this paper is to summarize the project results and emphasize the unmet research needs among patients with undiagnosed rare diseases in Korea.ResultsPatient enrollment, assessment, and diagnostic processes were determined by the KUDP clinical expert consortium. Patients followed a diagnostic workflow after being categorized into one of four groups: I) insufficient clinical information or lack of standard diagnostic processes; II) undiagnosed due to low disease awareness; III) clinically diagnosed but unconfirmed genetically due to genetic heterogeneities; or IV) unknown disease due to complex, atypical clinical presentations. After excluding two patients from group I, 97 patients were enrolled, including 10 in group II, 67 in group III, and 20 in group IV. Most of them (92 of 97, 94.8%) were pediatric patients (< 18 years old) and 59 (60.8%) were male. The primary symptoms for 80 patients (82.5%) were neurologic. During the one-year pilot study, 72 patients completed a diagnostic assessment including clinical and molecular genetic analyses; some patients also underwent pathological or biochemical analysis. Twenty-eight of these patients (28/72, 38.9%) achieved molecular genetic diagnosis. Thirteen patients were diagnosed based on traditional tests, including biochemical assay, single or targeted genetic analysis, and chromosomal microarray. We performed whole exome sequencing on 52 patients, among whom 15 (28.8%, 15/52) reached a final diagnosis. One new disorder was identified via international collaboration.ConclusionsUsing an efficient clinical diagnostic workflow, this KUDP pilot study resulted in a fair diagnostic success rate, improving the potential for additional diagnoses and new scientific discovery of complex and rare diseases. KUDP also satisfied unmet needs for rare diseases with multisystem involvement, highlighting the value of emerging genomic technologies for further research into rare and still-undiagnosed conditions.

A dileucine motif in the COOH-terminal domain of NKCC1 targets the cotransporter to the plasma membrane

Na+-K+-2Cl- cotransporter-1 (NKCC1) mediates the electroneutral transport of Na+, K+, and Cl- and is normally localized to the basolateral membrane of polarized epithelial cells. We recently reported the first known solute carrier family 12 member 2 ( SLC12A2) mutation (we call NKCC1-DFX) that causes epithelial dysfunction in an undiagnosed disease program case. The heterozygous mutation leads to truncation of the COOH-terminal tail of the cotransporter, resulting in both mutant and wild-type cotransporters being mistrafficked to the apical membrane of polarized epithelial cells. Here we demonstrate by using consecutive truncations and site-directed mutagenesis of the COOH-terminal domain of NKCC1 that truncation of NKCC1 COOH domain uncouples the cotransporter from the lateral membrane. We identify a dileucine motif that, when mutated, leads to cotransporter accumulation in the cytoplasm and mistrafficking to the apical/subapical region of epithelial cells, thereby recapitulating the phenotype observed with the patient mutation. We show that truncation deletion and LL substitution mutants are trafficked out of the endoplasmic reticulum and trans-Golgi network but accumulate in early and late endosomes where they are degraded.

Early infantile-onset epileptic encephalopathy 28 due to a homozygous microdeletion involving the WWOX gene in a region of uniparental disomy.

The genetic etiologies of many rare disorders, including early infantile epileptic encephalopathies, are largely undiagnosed. A 6-year-old girl was admitted to the National Institutes of Health Undiagnosed Diseases Program with profound intellectual disability, infantile-onset seizures, chronic respiratory failure, facial dysmorphisms, skeletal abnormalities, and atrial septum defect. A large region of homozygosity was discovered on chromosome 16, spanning 16q22.1-16q24.3' caused by uniparental disomy (UPD) that included a maternally inherited homozygous microdeletion covering exon 6 of WWOX (NM_016373.3). mRNA expression analysis revealed that the deletion led to nonsense-mediated decay of the NM_016373.3 transcript; the exon 6 of an alternative transcript (NM_130791.3), lacking the short-chain dehydrogenase, was utilized. The microdeletion in WWOX explains the seizures and intellectual disability, while pathogenic variants in another gene, HSPG2, are likely responsible for the patient's skeletal abnormalities. This report describes a rare autosomal recessive disorder with multiple genetic etiologies, one of which involves UPD.

Glycomics in rare diseases: from diagnosis tomechanism

The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) studies rare genetic disorders not only to achieve diagnoses, but to understand human biology. To ascertain the contribution of protein glycosylation to rare diseases, the NIH UDP used mass spectrometry to agnostically identify abnormalities of N-linked and O-linked glycans in plasma and free oligosaccharides in the urine of 207 patients. 60% of UDP patients had a glycome profile that deviated from control values in at least 1 fluid. Additional evaluation of the fibroblast glycome in 66 patients with abnormalities in plasma and/or urine revealed a consistent glycome phenotype in 83% of these cases. Many of these patients may have secondary glycosylation defects, since it is unlikely that they all have congenital disorders of glycosylation (CDGs). In fact, whole exome sequencing revealed only a few patients with CDGs, along with several others having disorders indirectly altering glycosylation. In summary, we describe a biochemical phenotyping screen to identify defects in protein glycosylation that can elucidate mechanisms of disease among NIH UDP patients.

SpainUDP: The Spanish Undiagnosed Rare Diseases Program

One of the IRDiRC goals for 2017–2027 is to achieve definitive diagnosis for rare undiagnosed diseases within one year, as delay in diagnosis remains one of the pending issues in the rare diseases field. The Spanish Undiagnosed Rare Diseases Program (SpainUDP) was created in response to this challenging scenario to cover patients’ needs and after seeing the success of the Undiagnosed Diseases Program (UDP) in the USA. SpainUDP offers a multidisciplinary approach to those patients who have long sought a diagnosis without any success. During the first phase of the protocol, undiagnosed cases are sent to SpainUDP by individual patients or families, patient organizations or hospitals. After careful analysis of phenotype, data from sequencing experiments (WES) is processed with a standard pipeline and detailed standardized phenotypic information (mapped to the Human Phenotype Ontology, HPO) is connected to genetic data. In addition, the participation of SpainUDP in international initiatives such as the European projects RD-Connect and Solve RD, the Undiagnosed Diseases Network International (UDNI), and the MatchMaker Exchange (MME) platform, allows the establishment of a global data sharing strategy across multiple projects submitting data to these international initiatives. From the official beginning of the program (at the end of 2015) until early 2018, 147 cases were accepted in SpainUDP. During this time, 37 cases (25%) dropped out the program due to several reasons. The remaining 110 cases are distributed as follows: phenotypic and genotypic (WES) characterization was finished in 30 cases, of which 20 (67%) were diagnosed; 21 cases are pending on variants’ validation by Sanger sequencing; in 25 cases, WES is ongoing and 34 cases are being studied for deep phenotypic characterization. In conclusion, SpainUDP aims to achieve a diagnosis following two recommendations of the IRDiRC: the patients’ diagnosis in as short a time as possible and the promotion of data sharing (especially genomic) at the international level.

A Novel Role for the Na‐K‐2Cl Cotransporter in Mitochondrial Respiration

A patient recruited by the undiagnosed disease program (UDP) at the NIH suffers from multi organ failure and deficits in energy homeostasis. The multi organ failure consists of complete gastrointestinal and bladder dysfunction, as well as thyroid, parathyroid, adrenal, and pancreatic deficiencies. The deficits in energy homeostasis were evidenced in lab tests conducted on the patient's muscle and liver biopsies, where there was an abnormal increase in glycogen content and mitochondrial DNA copy number. Whole exome sequencing showed that the patient expresses a de novo mutation in an allele of the Slc12a2 gene encoding the Na‐K‐2Cl cotransporter‐1 (NKCC1). Previous studies in the laboratory demonstrated that the 11 base pair deletion causing a truncation of the carboxyl‐terminus, leads to a non‐functional transporter. We have also demonstrated that the UDP patient's fibroblasts displayed reduced total NKCC1‐mediated K+ influx. Additionally, trafficking studies in transfected HEK293 cells expressing the NKCC1 truncation mutation have revealed that this mutated protein dimerizes with wild‐type (WT) NKCC1 and is trafficked to the plasma membrane along with WT NKCC1.To address a possible role of the cotransporter in metabolism, I utilized fibroblasts isolated from the patient and from healthy controls and performed mitochondrial respiration stress tests. I showed that mitochondrial respiration and ATP production was significantly higher in the patient's fibroblasts. Because the cells from the patient might carry additional mutations, I transfected MDCK cells with EGFP‐tagged wild‐type or mutant transporter, sorted the cells, and tested them. Cells expressing the mutant cotransporter also demonstrated higher mitochondrial respiration, compared to cells expressing wild‐type EGFP‐NKCC1.To further confirm the role of NKCC1 in mitochondrial respiration, I subjected control MDCK cells to bumetanide, a NKCC1 specific inhibitor. MDCK cells treated with 20 mM bumetanide for 20 min also demonstrated an increase in mitochondrial respiration. To further assess whether this effect in mitochondrial respiration is NKCC1 specific, I subjected bumetanide to two stable lines of MDCK cells (LK‐A3 and LK‐C1) that carry a distinct mutation in NKCC1, resulting in a non‐functional transporter. There was no change in mitochondrial respiration levels in these cells, which indicated that the rise in mitochondrial respiration levels in wild‐type cell is NKCC1 specific. These data reveal a novel role for NKCC1 in mitochondrial respiration. Future work will address the mechanism by which NKCC1 activity affects mitochondrial function.Support or Funding InformationSupported by NIH grants R21GM118944 and RO1DK093501This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Compound heterozygosity for loss-of-functionGARSvariants results in a multisystem developmental syndrome that includes severe growth retardation

Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes that ligate amino acids onto tRNA molecules. Genes encoding ARSs have been implicated in myriad dominant and recessive disease phenotypes. Glycyl-tRNA synthetase (GARS) is a bifunctional ARS that charges tRNAGly in the cytoplasm and mitochondria. GARS variants have been associated with dominant Charcot-Marie-Tooth disease but have not been convincingly implicated in recessive phenotypes. Here, we describe a patient from the NIH Undiagnosed Diseases Program with a multisystem, developmental phenotype. Whole-exome sequence analysis revealed that the patient is compound heterozygous for one frameshift (p.Glu83Ilefs*6) and one missense (p.Arg310Gln) GARS variant. Using in vitro and in vivo functional studies, we show that both GARS variants cause a loss-of-function effect: the frameshift variant results in depleted protein levels and the missense variant reduces GARS tRNA charging activity. In support of GARS variant pathogenicity, our patient shows striking phenotypic overlap with other patients having ARS-related recessive diseases, including features associated with variants in both cytoplasmic and mitochondrial ARSs; this observation is consistent with the essential function of GARS in both cellular locations. In summary, our clinical, genetic, and functional analyses expand the phenotypic spectrum associated with GARS variants.

Defining Disease, Diagnosis, and Translational Medicine within a Homeostatic Perturbation Paradigm: The National Institutes of Health Undiagnosed Diseases Program Experience.

Traditionally, the use of genomic information for personalized medical decisions relies on prior discovery and validation of genotype–phenotype associations. This approach constrains care for patients presenting with undescribed problems. The National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP) hypothesized that defining disease as maladaptation to an ecological niche allows delineation of a logical framework to diagnose and evaluate such patients. Herein, we present the philosophical bases, methodologies, and processes implemented by the NIH UDP. The NIH UDP incorporated use of the Human Phenotype Ontology, developed a genomic alignment strategy cognizant of parental genotypes, pursued agnostic biochemical analyses, implemented functional validation, and established virtual villages of global experts. This systematic approach provided a foundation for the diagnostic or non-diagnostic answers provided to patients and serves as a paradigm for scalable translational research.